You aren’t missing a font setting here you've actually run into a genuine integration bug.
To break down what's happening under the hood. HarfBuzz is fully capable of processing the OpenType jalt (Justification Alternates) feature, but HarfBuzz itself doesn’t handle paragraph justification. Its only job is to shape the text runs it's given. It’s up to InDesign’s paragraph composer to figure out where those justification alternates are needed, and then explicitly pass those specific character ranges over to HarfBuzz.
In fact, the OpenType spec explicitly puts this responsibility on the host application. The jalt feature is supposed to be triggered by the justification algorithm, which then calculates the new line lengths during composition.
Because this works perfectly fine with Adobe’s legacy shaping engine but gets completely ignored by HarfBuzz, it strongly points to a regression in how InDesign integrates with HarfBuzz, rather than an issue with the OpenType fonts themselves. Adobe’s documentation still lists Justification Alternates as a supported World-Ready feature (specifically naming fonts like Adobe Arabic, Myriad Arabic, and Adobe Naskh) with no mention of an exception for HarfBuzz that I can find.
The Temporary Workaround
For now, your best bet is to revert to the old behaviour:
Go to Preferences > Advanced Type and check Enable Legacy Text Shaping for Adobe World-Ready Composer.
This is Adobe’s official fallback for rendering issues, but keep in mind that switching shaping engines can cause text to reflow. Definitely double-check your documents for altered line endings, overset text, or pagination shifts before sending anything to print or export.
Filing the Bug Report
This is absolutely worth reporting as a reproducible InDesign bug. To give it the best chance of getting fixed, I'd recommend creating a minimal test document using a standard font like Adobe Naskh and listing these steps:
Apply the World-Ready Paragraph Composer.
Fully justify the Arabic paragraph.
Enable Justification Alternates.
Compare the broken result under HarfBuzz with the correct result under Legacy Text Shaping.
Report here
https://indesign.uservoice.com/forums/601180-adobe-indesign-bugs
I’d frame it as “Justification Alternates (jalt) ignored by the HarfBuzz World-Ready shaping workflow” rather than saying the feature fails for all OpenType fonts. Since only specific fonts actually include the jalt feature, narrowing it down to the HarfBuzz integration will help the engineering team pinpoint the issue much faster.